I think you're overthinking it a little. Storm has lightning powers so it could be cool to see Thor meet another lightning user. Thor has spent plenty of time on Earth before, it's no more bizarre for him to end up in Kenya than it is for him to end up in London or New Mexico.
I definitely think we'll see mutants in other MCU films and shows for a few years before an X-men film. And I think Storm is a big enough character that they'll want to make her both a main X-woman and a major player in the MCU at large. Could easily see Storm appearing in Thor 4 and BP2 before X-men.
But Storm doesn't really have anything to do with Thor outside of having lightning powers (I know she was a member of Thor corps in the comics but that was decades after she was established-- hence why I used the Kitty GOTG)
If Ororo is already a fully independent character going on cosmic adventures with Asgardians and fighting god killers, then ending up at a school with a rag-tag group of mutants is a massive downgrade. It's like having Valkyrie show up
The X-Men and the school are meant for mutants who don't feel whole. Whether that's control, emotional support, self discovery, or a surrogate family. That's why I'd prefer she be introduced in Black Panther II--Maybe as princess of a Wakandan tribe (Xavier can show up since their borders are open now).
So we are introduced to an incomplete Ororo whose void can be filled at the school, and whose calling can be discovered with the X-Men.
But does this serve Thor or Ororo?
If Storm is going to be a major player, her introduction should be impactful, meaningful and respectful. Not an afterthought.
It def serves the movie's spectacle. And knowing Waititi, his vision of Storm is likely going to be a comedic parody of herself. And whoever gets X-Men is going to be saddled with his vision
Coogler should def get that opportunity to define MCU Storm; root her in her culture, in her goddess mythology. Showcase her power a little bit but also show that something is missing, that there is a void she needs to fill.
After she's been with the X-Men, I'd be completely fine with her teaming up with Thor. But not as an introduction